---
title: "Chick Weight Data"
output: 
  flexdashboard::flex_dashboard:
    orientation: columns
    vertical_layout: fill
    social: menu
    source_code: embed
---

```{r setup, include=FALSE}
# Install the latest packages via github
# devtools::install_github("rstudio/crosstalk")
# devtools::install_github("rstudio/DT")
# devtools::install_github("rstudio/flexdashboard")

library(flexdashboard)
library(tidyverse)
library(DT)
library(crosstalk)
library(knitr)
library(rmarkdown)
```

```{r CWPrep}
## Convert ChickWeight data into a tibble with desirable properties
CW <- ChickWeight %>%
  as_tibble() %>%
  mutate(Chick = as.numeric(as.character(Chick))) %>% 
  mutate(Diet = paste("Diet", as.character(Diet))) %>%
  rename(Weight = weight) %>%
  select(Chick, Diet, Time, Weight) %>%
  arrange(Chick, Diet, Time)

## Range for the slider App
rWgt <- range(CW$Weight)

# Summary Statistics by Diet and Time
CW_sum_stats <- CW %>% 
  group_by(Diet, Time) %>%
  summarise(N = n(),
            Mean = mean(Weight),
            SD = sd(Weight),
            Min = min(Weight),
            Median = median(Weight),
            Max = max(Weight))
```

Raw Data
=====================================

```{r rawData}
# Wrap data frame in SharedData
sdCW <- SharedData$new(CW)

# Use SharedData like a dataframe with Crosstalk-enabled widgets
bscols(widths = c(3, NA),
       list(
         filter_select("Chick", "Chick IDs", sdCW, ~Chick, multiple = TRUE), 
         filter_checkbox("Diet", "Diets", sdCW, ~Diet, columns = 2), 
         filter_select("Time", "Time (Days)", sdCW, ~Time, multiple = TRUE), 
         filter_slider("Weight", "Weight", sdCW, column=~Weight, width = "100%")
       ),
       datatable(sdCW, rownames = FALSE, 
            options = list(columnDefs = list(list(className = 'dt-center', targets = 0:1)), 
              pageLength = 15, deferRender=TRUE, scrollY="100%", scroller=TRUE))
)
```


Summary Stats
=====================================


```{r sumStats}
# Wrap data frame in SharedData
sdCWss <- SharedData$new(CW_sum_stats)

# Use SharedData like a dataframe with Crosstalk-enabled widgets
bscols(widths = c(3, NA),
       list(
         filter_checkbox("Diet", "Diets", sdCWss, ~Diet, columns = 2), 
         filter_select("Time", "Time (Days)", sdCWss, ~Time, multiple = TRUE)
       ),
       datatable(sdCWss, rownames = FALSE, 
            options = list(columnDefs = list(list(className = 'dt-center', targets = 0)), 
                           pageLength = 15, deferRender=TRUE, scrollY="100%", scroller=TRUE)) %>% 
         DT::formatRound(c('Mean', 'SD', 'Median'), digits = c(1, 2, 1))
)


```


   
Graphs
=====================================

Column  {.tabset .tabset-fade}
-------------------------------------

```{r basicPlot}
g <- ggplot(CW, aes(Time, Weight, colour = Diet)) +
  scale_x_continuous(breaks=unique(CW$Time)) +
  scale_y_continuous(breaks=seq(50, 350, by = 50)) +
  xlab("Time (days)") + 
  ylab("Weight (grams)") 
```


### Mean Lines (1)

```{r meanLines1}
g +
  geom_jitter(size = .4, width = 0.2) +
  stat_summary(fun.y="mean", geom="line", aes(group=Diet), size=1) +
  theme(legend.position = "bottom")
```

### Mean Lines (4)

```{r meanLines4}
g +
  facet_wrap(~Diet) +
  geom_jitter(size = .4, width = 0.2) +
  stat_summary(fun.y="mean", geom="line", aes(group=Diet), size=1) +
  theme(legend.position = "none")
```

### Box Whisker Plot (1)

```{r bwPlot1}
g +
  geom_boxplot(aes(group=interaction(Time, Diet))) +
  theme(legend.position = "bottom")
```

### Box Whisker Plot (4)

```{r bwPlot4}
g +
  facet_wrap(~Diet) +
  geom_boxplot(aes(group=interaction(Time, Diet))) +
  theme(legend.position = "none")
```

R Help
=====================================

```{r rHelp}
# This is not pretty but needs to be improved.
helpCW <- help("ChickWeight")
hcw <- tools:::Rd2txt(utils:::.getHelpFile(as.character(helpCW))) 
  cat(gsub("_", "", hcw, fixed = TRUE))
```